Significant volume defects are observed on rubber/silica nano-filler composites under large deformations such as during extrusion process. To understand the causes of the instabilities, structure and rheological properties of these nanocomposites have been studied especially by NMR spectroscopy and by relaxation and elongation measurements. The effect of blend composition and mixing conditions on the structure and rheological properties of the rubber/silica composites was investigated. Blends with and without agents such as a polysulfide silane (TESPT) or Octeo were prepared in internal mixer under different experimental conditions (variation of dump temperature or rotation speed). In presence of silane, silica aggregates can be grafted to rubber chains whereas Octeo only react with silica. The grafting of these agents on silica surface induces the improvement of the silica aggregates dispersion thanks to the reduction of filler-filler interactions. In silane blends, NMR spectroscopy allowed the quantification of the silane/rubber grafting and highlighted the presence of unwelcome pre-crosslinking reactions between rubber chains at high mixing temperature. Therefore different kinds of filler/rubber networks can be noted according to the nature of the agent (silane or Octeo) and to the mixing parameters. Then rheological properties of blends can be linked to the nature of their filler/rubber network. Thereby, elongation measurements and relaxation times showed a strong impact of these networks on the viscoelastic behavior over the whole range of time. Finally, a correlation can be highlighted between the blend structure, its rheology and the emergence of volume defects during extrusion.